+Open data
-Basic information
Entry | Database: PDB / ID: 2obh | ||||||
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Title | Centrin-XPC peptide | ||||||
Components |
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Keywords | CELL CYCLE / DNA REPAIR COMPLEX EF HAND SUPERFAMILY PROTEIN-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / 9+2 motile cilium / nucleotide-excision repair complex / photoreceptor connecting cilium / DNA damage sensor activity / centriole replication / heterotrimeric G-protein binding ...heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / 9+2 motile cilium / nucleotide-excision repair complex / photoreceptor connecting cilium / DNA damage sensor activity / centriole replication / heterotrimeric G-protein binding / transcription export complex 2 / response to auditory stimulus / nuclear pore nuclear basket / bubble DNA binding / UV-damage excision repair / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / regulation of mitotic cell cycle phase transition / site of DNA damage / mRNA transport / mismatch repair / SUMOylation of DNA damage response and repair proteins / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / ciliary basal body / regulation of cytokinesis / nucleotide-excision repair / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding / Formation of Incision Complex in GG-NER / Regulation of PLK1 Activity at G2/M Transition / protein transport / apical part of cell / mitotic cell cycle / single-stranded DNA binding / spermatogenesis / microtubule binding / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / response to xenobiotic stimulus / cell division / intracellular membrane-bounded organelle / DNA repair / centrosome / calcium ion binding / positive regulation of DNA-templated transcription / chromatin / protein-containing complex binding / nucleolus / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Charbonnier, J.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural, thermodynamic, and cellular characterization of human centrin 2 interaction with xeroderma pigmentosum group C protein. Authors: Charbonnier, J.B. / Renaud, E. / Miron, S. / Le Du, M.H. / Blouquit, Y. / Duchambon, P. / Christova, P. / Shosheva, A. / Rose, T. / Angulo, J.F. / Craescu, C.T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and preliminary X-ray diffraction data of the complex between human centrin 2 and a peptide from the protein XPC Authors: Charbonnier, J.B. / Christova, P. / Shosheva, A. / Le Du, E. / Stura, M.H. / Blouquit, Y. / Duchambon, P. / Miron, S. / Craescu, C.T. #2: Journal: Biochemistry / Year: 2006 Title: Flexibility and plasticity of human centrin 2 binding to the xeroderma pigmentosum group C protein (XPC) from nuclear excision repair Authors: Yang, A. / Miron, S. / Mouawad, L. / Duchambon, P. / Blouquit, Y. / Craescu, C.T. #3: Journal: J.Biol.Chem. / Year: 2006 Title: The structure of the human centrin 2-xeroderma pigmentosum group C protein complex Authors: Thompson, J.R. / Ryan, Z.C. / Salisbury, J.L. / Kumar, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2obh.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2obh.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 2obh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2obh_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 2obh_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 2obh_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2obh_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/2obh ftp://data.pdbj.org/pub/pdb/validation_reports/ob/2obh | HTTPS FTP |
-Related structure data
Related structure data | 1topS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 16491.637 Da / Num. of mol.: 2 / Fragment: HsCen2 ( Residues: 26-168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CETN2, CALT, CEN2 / Plasmid: PET24A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41208 #2: Protein/peptide | Mass: 2139.677 Da / Num. of mol.: 2 / Fragment: XPC fragment (Residues: 847-863) / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS IN HOMO SAPIENS / References: UniProt: Q01831 #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 30% MPEG 550, 0.1M NaCl, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→52.4 Å / Num. obs: 34221 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 20.95 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4768 / Rsym value: 0.395 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TOP Resolution: 1.8→52.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.353 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.348 Å2
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Refine analyze | Luzzati coordinate error obs: 0.237 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→52.4 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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